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- PDB-4lj1: RipD (Rv1566c) from Mycobacterium tuberculosis: a non-catalytic N... -

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Basic information

Entry
Database: PDB / ID: 4lj1
TitleRipD (Rv1566c) from Mycobacterium tuberculosis: a non-catalytic NlpC/p60 domain protein with two penta-peptide repeat units (PVQQA-PVQPA)
ComponentsInvasion-associated protein
KeywordsCELL INVASION / NlpC/P60 / Cell wall stabilisation / periplasmic
Function / homology
Function and homology information


: / NlpC/P60 domain profile. / Endopeptidase, NLPC/P60 domain / NlpC/P60 family / endopeptidase domain like (from Nostoc punctiforme) / endopeptidase fold (from Nostoc punctiforme) / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Possible Inv protein
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.17 Å
AuthorsBoth, D. / Steiner, E.M. / Linder, D.C. / Schnell, R. / Schneider, G.
CitationJournal: Biochem.J. / Year: 2014
Title: RipD (Rv1566c) from Mycobacterium tuberculosis: adaptation of an NlpC/p60 domain to a non-catalytic peptidoglycan-binding function.
Authors: Both, D. / Steiner, E.M. / Izumi, A. / Schneider, G. / Schnell, R.
History
DepositionJul 4, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Invasion-associated protein


Theoretical massNumber of molelcules
Total (without water)15,4391
Polymers15,4391
Non-polymers00
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.247, 30.752, 61.921
Angle α, β, γ (deg.)90.00, 120.85, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Invasion-associated protein


Mass: 15438.562 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 38-182
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: RVBD_1566c / Production host: Escherichia coli (E. coli) / References: UniProt: O06624
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 42.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: 0.1M Tris/HCl pH 7.9, 0.2M Trimethylamine N-oxide, 20% PEG 2000 MME, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 26, 2013
RadiationMonochromator: horizontally diffracting Si (111) monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.17→53.16 Å / Num. all: 43924 / Num. obs: 43616 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.17-1.69196.5
1.69-53.16199.3

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Processing

Software
NameVersionClassification
DNAdata collection
MOLREPphasing
REFMAC5.6.0117refinement
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.17→53.16 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.092 / SU ML: 0.022 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.034 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16648 2221 5.1 %RANDOM
Rwork0.14672 ---
obs0.14773 41701 99.32 %-
all-43924 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.969 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å2-0 Å2-0.07 Å2
2--0.21 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.17→53.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms997 0 0 139 1136
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.021076
X-RAY DIFFRACTIONr_bond_other_d0.0010.02743
X-RAY DIFFRACTIONr_angle_refined_deg1.4411.9711473
X-RAY DIFFRACTIONr_angle_other_deg0.9331820
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0685151
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.48923.33342
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.31515174
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.215158
X-RAY DIFFRACTIONr_chiral_restr0.0930.2163
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211231
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02221
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr3.10531819
X-RAY DIFFRACTIONr_sphericity_free25.397548
X-RAY DIFFRACTIONr_sphericity_bonded8.41751880
LS refinement shellResolution: 1.169→1.199 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 139 -
Rwork0.28 2764 -
obs--93.1 %

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